GenomicAlignments (version 1.8.4)

GAlignmentsList-class: GAlignmentsList objects

Description

The GAlignmentsList class is a container for storing a collection of GAlignments objects.

Constructor

GAlignmentsList(...): Creates a GAlignmentsList from a list of GAlignments objects.

Accessors

In the code snippets below, x is a GAlignmentsList object.

length(x): Return the number of elements in x.

names(x), names(x) <- value: Get or set the names of the elements of x.

seqnames(x), seqnames(x) <- value: Get or set the name of the reference sequences of the alignments in each element of x.

rname(x), rname(x) <- value: Same as seqnames(x) and seqnames(x) <- value.

strand(x), strand(x) <- value: Get or set the strand of the alignments in each element of x.

cigar(x): Returns a character list of length length(x) containing the CIGAR string for the alignments in each element of x.

qwidth(x): Returns an integer list of length length(x) containing the length of the alignments in each element of x *after* hard clipping (i.e. the length of the query sequence that is stored in the corresponding SAM/BAM record).

start(x), end(x): Returns an integer list of length length(x) containing the "start" and "end" (respectively) of the alignments in each element of x.

width(x): Returns an integer list of length length(x) containing the "width" of the alignments in each element of x.

njunc(x): Returns an integer list of length x containing the number of junctions (i.e. N operations in the CIGAR) for the alignments in each element of x.

seqinfo(x), seqinfo(x) <- value: Get or set the information about the underlying sequences. value must be a Seqinfo object.

seqlevels(x), seqlevels(x) <- value: Get or set the sequence levels of the alignments in each element of x.

seqlengths(x), seqlengths(x) <- value: Get or set the sequence lengths for each element of x. seqlengths(x) is equivalent to seqlengths(seqinfo(x)). value can be a named non-negative integer or numeric vector eventually with NAs.

isCircular(x), isCircular(x) <- value: Get or set the circularity flags for the alignments in each element in x. value must be a named logical list eventually with NAs.

genome(x), genome(x) <- value: Get or set the genome identifier or assembly name for the alignments in each element of x. value must be a named character list eventually with NAs.

seqnameStyle(x): Get or set the seqname style for alignments in each element of x.

Coercion

In the code snippets below, x is a GAlignmentsList object.

granges(x, use.names=TRUE, use.mcols=FALSE, ignore.strand=FALSE), ranges(x, use.names=TRUE, use.mcols=FALSE): Return either a GRanges or a IRanges object of length length(x). Note this coercion IGNORES the cigar information. The resulting ranges span the entire range, including any junctions or spaces between paired-end reads. If use.names is TRUE, then the names on x (if any) are propagated to the returned object. If use.mcols is TRUE, then the metadata columns on x (if any) are propagated to the returned object. granges coercion supports ignore.strand to allow ranges of opposite strand to be combined (see examples). All ranges in the resulting GRanges will have strand ‘*’.

grglist(x, use.names=TRUE, use.mcols=FALSE, ignore.strand=FALSE), rglist(x, use.names=TRUE, use.mcols=FALSE): Return either a GRangesList or an IRangesList object of length length(x). This coercion RESPECTS the cigar information. The resulting ranges are fragments of the original ranges that do not include junctions or spaces between paired-end reads. If use.names is TRUE, then the names on x (if any) are propagated to the returned object. If use.mcols is TRUE, then the metadata columns on x (if any) are propagated to the returned object. grglist coercion supports ignore.strand to allow ranges of opposite strand to be combined (see examples). When ignore.strand is TRUE all ranges in the resulting GRangesList have strand ‘*’.

as(x, "GRanges"), as(x, "Ranges"), as(x, "GRangesList"), as(x, "RangesList"): Alternate ways of doing granges(x, use.names=TRUE, use.mcols=TRUE), ranges(x, use.names=TRUE, use.mcols=TRUE), grglist(x, use.names=TRUE, use.mcols=TRUE), and rglist(x, use.names=TRUE, use.mcols=TRUE), respectively.

as.data.frame(x, row.names = NULL, optional = FALSE, ..., value.name = "value", use.outer.mcols = FALSE, group_name.as.factor = FALSE): Coerces x to a data.frame. See as.data.frame on the List man page for details (?List).

as(x, "GALignmentsList"): Here x is a GAlignmentPairs object. Return a GAlignmentsList object of length length(x) where the i-th list element represents the ranges of the i-th alignment pair in x.

Subsetting and related operations

In the code snippets below, x is a GAlignmentsList object.

x[i], x[i] <- value: Get or set list elements i. i can be a numeric or logical vector. value must be a GAlignments.

x[[i]], x[[i]] <- value: Same as x[i], x[i] <- value.

x[i, j], x[i, j] <- value: Get or set list elements i with optional metadata columns j. i can be a numeric, logical or missing. value must be a GAlignments.

Combining

c(...): Concatenates the GAlignmentsList objects in ....

Details

A GAlignmentsList object contains a list of GAlignments objects. The majority of operations on this page are described in more detail on the GAlignments man page, see ?GAlignments.

References

http://samtools.sourceforge.net/

See Also

• readGAlignmentsList for reading genomic alignments from a file (typically a BAM file) into a GAlignmentsList object.

• GAlignments and GAlignmentPairs objects for handling aligned single- and paired-end reads, respectively.

• junctions-methods for extracting and summarizing junctions from a GAlignmentsList object.

• findOverlaps-methods for finding range overlaps between a GAlignmentsList object and another range-based object.

• seqinfo in the GenomeInfoDb package for getting/setting/modifying the sequence information stored in an object.

• The GRanges and GRangesList classes defined and documented in the GenomicRanges package.

Examples

gal1 <- GAlignments(
    seqnames=Rle(factor(c("chr1", "chr2", "chr1", "chr3")),
        c(1, 3, 2, 4)),
    pos=1:10, cigar=paste0(10:1, "M"),
    strand=Rle(strand(c("-", "+", "*", "+", "-")), c(1, 2, 2, 3, 2)),
    names=head(letters, 10), score=1:10)

gal2 <- GAlignments(
    seqnames=Rle(factor(c("chr2", "chr4")), c(3, 4)), pos=1:7,
    cigar=c("5M", "3M2N3M2N3M", "5M", "10M", "5M1N4M", "8M2N1M", "5M"),
    strand=Rle(strand(c("-", "+")), c(4, 3)),
    names=tail(letters, 7), score=1:7)

galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)


## ---------------------------------------------------------------------
## A. BASIC MANIPULATION
## ---------------------------------------------------------------------

length(galist)
names(galist)
seqnames(galist)
strand(galist)
head(cigar(galist))
head(qwidth(galist))
head(start(galist))
head(end(galist))
head(width(galist))
head(njunc(galist))
seqlevels(galist)

## Rename the reference sequences:
seqlevels(galist) <- sub("chr", "seq", seqlevels(galist))
seqlevels(galist)

grglist(galist)  # a GRangesList object
rglist(galist)   # an IRangesList object

## ---------------------------------------------------------------------
## B. SUBSETTING
## ---------------------------------------------------------------------

galist[strand(galist) == "-"]
has_junctions <- sapply(galist,
                        function(x) any(grepl("N", cigar(x), fixed=TRUE)))
galist[has_junctions]

## Different ways to subset:
galist[2]             # a GAlignments object of length 1
galist[[2]]           # a GAlignments object of length 1
grglist(galist[2])  # a GRangesList object of length 1
rglist(galist[2])   # a NormalIRangesList object of length 1

## ---------------------------------------------------------------------
## C. mcols()/elementMetadata()
## ---------------------------------------------------------------------

## Metadata can be defined on the individual GAlignment elements
## and the overall GAlignmentsList object. By default, 'level=between' 
## extracts the GALignmentsList metadata. Using 'level=within' 
## will extract the metadata on the individual GAlignments objects.

mcols(galist) ## no metadata on the GAlignmentsList object
mcols(galist, level="within")


## ---------------------------------------------------------------------
## D. readGAlignmentsList()
## ---------------------------------------------------------------------

library(pasillaBamSubset)

## 'file' as character.
fl <- untreated3_chr4()
galist1 <- readGAlignmentsList(fl)

galist1[1:3]
length(galist1)
table(elementNROWS(galist1))

## When 'file' is a BamFile, 'asMates' must be TRUE. If FALSE,
## the data are treated as single-end and each list element of the
## GAlignmentsList will be of length 1. For single-end data 
## use readGAlignments() instead of readGAlignmentsList().
bf <- BamFile(fl, yieldSize=3, asMates=TRUE)
readGAlignmentsList(bf)

## Use a 'param' to fine tune the results.
param <- ScanBamParam(flag=scanBamFlag(isProperPair=TRUE))
galist2 <- readGAlignmentsList(fl, param=param)
length(galist2)


## ---------------------------------------------------------------------
## E. COERCION 
## ---------------------------------------------------------------------

## The granges() and grlist() coercions support 'ignore.strand' to 
## allow ranges from different strands to be combined. In this example 
## paired-end reads aligned to opposite strands were read into a 
## GAlignmentsList. If the desired operation is to combine these ranges, 
## regardless of junctions or the space between pairs, 'ignore.strand'
## must be TRUE.
granges(galist[1])
granges(galist[1], ignore.strand=TRUE)

## grglist()
galist <- GAlignmentsList(noGaps=gal1, Gaps=gal2)
grglist(galist)
grglist(galist, ignore.strand=TRUE)